Simultaneous electrochemical determination of two analytes based on nuclease-assisted target recycling amplification

In the present study, a method for simultaneous determination of two different DNAs is developed based on nuclease-assisted target recycling and nanoparticle amplification. The target recycling process is accomplished by taking advantage of the cleavage property of nicking endonuclease (NEase) for specific nucleotide sequences in duplex. In the presence of target DNA, the linker DNA in our detection system can hybridize with the target and be cleaved to form short fragments. Thus the target DNA is released and recognized by another linker DNA, activating the next round of cleavage reaction. On the other hand, two bio-barcode probes, a PbS nanoparticles (NPs)-DNA probe and a CdS NPs-DNA probe, are used for tracing two target DNAs to further amplify the detection signals. Based on a sensitive differential pulse anodic stripping voltammetry (DPASV) method for the simultaneous detection of Pb²⁺ and Cd²⁺ obtained by dissolving two probes, two different target DNAs are determined with high sensitivity and single-base mismatch selectivity.     

A simple and ultrasensitive electrochemical DNA biosensor based on DNA concatamers

A simple, ultrasensitive and selective electrochemical DNA biosensor based on DNA concatamers is described, which can detect as low as 100 aM target DNA even in complex samples.     

An electrochemical DNA biosensor based on the "Y" junction structure and restriction endonuclease-aided target recycling strategy

Based on the "Y" junction structure and restriction endonuclease-aided target recycling strategy, an electrochemical biosensor for DNA detection was developed. This universal biosensor was suitable for detecting different sequences of target DNA by changing the sequence of capture and assistant strands.     

Colorimetric detection of genetically modified organisms based on exonuclease III-assisted target recycling and hemin/G-quadruplex DNAzyme amplification

An isothermal colorimetric method is described for amplified detection of the CaMV 35S promoter sequence in genetically modified organism (GMO). It is based on (a) target DNA-triggered unlabeled molecular beacon (UMB) termini binding, and (b) exonuclease III (Exo III)-assisted target recycling, and (c) hemin/G-quadruplex (DNAzyme) based signal amplification. The specific binding of target to the G-quadruplex sequence-locked UMB triggers the digestion of Exo III. This, in turn, releases an active G-quadruplex segment and target DNA for successive hybridization and cleavage. The Exo III impellent recycling of targets produces numerous G-quadruplex sequences. These further associate with hemin to form DNAzymes and hence will catalyze H₂O₂-mediated oxidation of the chromogenic enzyme substrate ABTS^2? causing the formation of a green colored product. This finding enables a sensitive colorimetric determination of GMO DNA (at an analytical wavelength of 420 nm) at concentrations as low as 0.23 nM. By taking advantage of isothermal incubation, this method does not require sophisticated equipment or complicated syntheses. Analyses can be performed within 90 min. The method also discriminates single base mismatches. In our perception, it has a wide scope in that it may be applied to the detection of many other GMOs.

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Graphical abstract An isothermal and sensitive colorimetric method is described for amplified detection of CaMV 35S promoter sequence in genetically modified organism (GMO). It is based on target DNA-triggered molecular beacon (UMB) termini-binding and exonuclease III assisted target recycling, and on hemin/G-quadruplex (DNAzyme) signal amplification.

     

A universal electrochemical biosensor for the highly sensitive determination of microRNAs based on isothermal target recycling amplification and a DNA signal transducer triggered reaction

MicroRNAs (miRNAs) play a considerable role in cancer occurrence and development, and have been identified as promising noninvasive biomarkers. The authors describe a voltammetric method for the determination of the cancer biomarker microRNA-21 (miRNA). It is based on a combination of a universal DNA signal transducer and isothermal target recycling amplification. A hairpin capture probe is bound to the target miRNA to form a duplex structure and to create a toehold in the transducer for initiating the target recycling amplification reaction. In contrast to traditional capture probes, a mismatched site is introduced to improve its ability to capture the target. In order to reduce the complex design procedures of the sequence and widen the applicability of this method, a signal transducer is introduced. Under optimal conditions, response to target miRNA is linear in the 0.5 to 2000 pM concentration range, with a 56 fM. detection limit (at an S/N ratio of 3). In order to characterize the process of target recycling and the stepwise modification of the electrode, real-time fluorescence, agarose gel electrophoresis, cyclic voltammetry, electrochemical impedance spectroscopy and chronocoulometry were used. The results indicate that this isothermal target recycling amplification results in an electrochemical biosensing scheme with wide potential for sensing other bioanalytes.

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Graphical abstract Schematic illustration of the electrochemical biosensing platform for miRNA-21 detection based on isothermal target recycling amplification and DNA signal transducer triggered strategy.

     

Label-free fluorescent biosensor based on the target recycling and Thioflavin T-induced quadruplex formation for short DNA species of c-erbB-2 detection

Non-invasive early diagnosis of breast cancer is the most effective way to improve the survival rate and increase more chances of breast-conserving. In this paper, we developed a label-free fluorescent biosensor based on nuclease assisted target recycling and Thioflavin T-induced quadruplex formation for short DNA species of c-erbB-2 detection in saliva. By employing the strategy, the sensor can detect as low as 20 fM target DNA with high discrimination ability even against single-base mismatch sequence. To the best of our knowledge, the proposed sensor is the first attempt to apply Thioflavin T that possesses outstanding structural selectivity for G-quadruplex in DNA amplification techniques, which may represent a promising path toward direct breast cancer detection in saliva at the point of care.     

Electrochemical biosensor based on hairpin DNA probe using 2-nitroacridone as electrochemical indicator for detection of DNA species related to Chronic Myelogenous Leukemia

In this article, a new kind of hairpin DNA Electrochemical biosensor using nitroacridone as electrochemical indicator was first designed, and used to detect BCR/ABL fusion gene in Chronic Myelogenous Leukemia (CML). The results indicated that in pH 7.0 Tris–HCl buffer solution, the oxidation peak current was linear with the concentration of complementary strand in the range of 6.2 × 10⁻⁸–3.1 × 10⁻⁷ mol/l with a detection limit of 5.3 × 10⁻⁹ mol/l. This new hairpin DNA electrochemical biosensor demonstrates its excellent specificity for single-base mismatch and complementary (dsDNA) after hybridization, and this probe has been used for assay of PCR product of a real sample with satisfactory result.     

An electrochemical biosensor based on DNA “nano-bridge” for amplified detection of exosomal microRNAs

Exosomal miRNAs, as potential biomarkers in liquid biopsy for cancer early diagnosis, have aroused widespread concern. Herein, an electrochemical biosensor based on DNA “nano-bridge” was designed and applied to detect exosomal microRNA-21 (miR-21) derived from breast cancer cells. In brief, the target miR-21 can specifically open the hairpin probe 1(HP1) labeled on the gold electrode (GE) surface through strand displacement reaction. Thus the exposed loop region of HP1 can act as an initiator sequence to activate the hybridization chain reaction (HCR) between two kinetically trapped hairpin probes: HP2 immobilized on the GE surface and biotin labeled HP3 in solution. Cascade HCR leads to the formation of DNA “nano-bridge” tethered to the GE surface with a great deal of “piers”. Upon addition of avidin-modified horseradish peroxidase (HRP), numerous HRP were bound to the formed “nano-bridge” through biotin-avidin interaction to arouse tremendous current signal. In theory, only a single miR-21 is able to trigger the continuous HCR between HP2 and HP3 until all of the HP2 are exhausted. Therefore the proposed biosensor achieved ultrahigh sensitivity toward miR-21 with the detection limit down to 168 amol/L, as well as little cross-hybridization even at the single-base-mismatched level. Successful attempts were also made in the detection of exosomal miR-21 obtained from the MCF-7 of breast cancer cell line. To our knowledge, this is the first attempt to built horizontal DNA nano-structure on the electrode surface for exosomal miRNAs detection. In a word, the high sensitivity, selectivity, low cost make the proposed method hold great potential application for early point-of-care (POC) diagnostics of cancer.     

Rolling circle amplification based amperometric aptamer/immuno hybrid biosensor for ultrasensitive detection of Vibrio parahaemolyticus

Microchimica Acta - The authors describe an antibody-aptamer based hetero-sandwich amperometric biosensor for the foodborne pathogen Vibrio parahaemolyticus. Antibody on the surface of a gold...     

A sensitive fluorescence strategy for telomerase detection in cancer cells based on T7 exonuclease-assisted target recycling amplification

A sensitive fluorescence strategy based on T7 exonuclease-assisted target recycling amplification was developed for telomerase detection in cancer cells. The novel strategy improved the fluorescence signal and sensitivity compared with the previously reported methods.     

Ultrasensitive electrochemical biosensor for specific detection of DNA based on molecular beacon mediated circular strand displacement polymerization and hyperbranched rolling circle amplification

Using a cascade signal amplification strategy, an ultrasensitive electrochemical biosensor for specific detection of DNA based on molecular beacon (MB) mediated circular strand displacement polymerization (CSDP) and hyperbranched rolling circle amplification (HRCA) was proposed. The hybridization of MB probe to target DNA resulted in a conformational change of the MB and triggered the CSDP in the presence of bio-primer and Klenow fragment (KF exo⁻), leading to multiple biotin-tagged DNA duplex. Furthermore, the HRCA was implemented to product amounts of double-stranded DNA (ds-DNA) fragments using phi29 DNA polymerase via biotin-streptavidin interaction. After the product of HRCA binded numerous biotinylated detection probes, an ultrasensitive electrochemical readout by further employing the streptavidin-alkaline phosphatase. The proposed biosensor exhibited excellent detection sensitivity and specificity with a log-linear response to target DNA from 0.01 fM to 10 pM as low as 8.9 aM. The proposed method allowed DNA detection with simplicity, rapidness, low cost and high specificity, which might have the potential for application in clinical molecular diagnostics and environmental monitoring.     

An electrochemical aptasensor for thrombin detection based on the recycling of exonuclease III and double-stranded DNA-templated copper nanoparticles assisted signal amplification

In this paper, we report an improved electrochemical aptasensor based on exonuclease III and double-stranded DNA (dsDNA)-templated copper nanoparticles (CuNPs) assisted signal amplification. In this sensor, duplex DNA from the hybridization of ligated thrombin-binding aptamer (TBA) subunits and probe DNA can act as an effective template for the formation of CuNPs on the electrode surface, so copper ions released from acid-dissolution of CuNPs may catalyze the oxidation of ο-phenylenediamine to produce an amplified electrochemical response. In the presence of thrombin, a short duplex domain with four complementary base pairs can be stabilized by the binding of TBA subunits with thrombin, in which TBA subunit 2 can be partially digested from 3′ terminal with the cycle of exonuclease III, so the ligation of TBA subunits and the subsequent formation of CuNPs can be inhibited. By electrochemical characterization of dsDNA-templated CuNPs on the electrode surface, our aptasensor can display excellent performances for the detection of thrombin in a broad linear range from 100 fM to 1 nM with a low detection limit of 20.3 fM, which can also specially distinguish thrombin in both PBS and serum samples. Therefore, our aptasensor might have great potential for clinical diagnosis of biomarkers in the future.     

An ultrasensitive electrochemical DNA sensor based on the ssDNA-assisted cascade of hybridization reaction

We have developed a simple and ultrasensitive E-DNA sensor based on the ssDNA-assisted cascade of a hybridization reaction mechanism to form a long concatamers structure to improve its sensitivity, significantly. The proposed sensor was applied to sequence-specific DNA and ATP detection. Experimental results showed a quantitative measurement with the detection limit as low as 1 aM for specific DNA and 10 fM for ATP.     

Exonuclease-assisted cascaded recycling amplification for label-free detection of DNA

The network consisting of three kinds of unlabeled stem-loop DNA molecular beacons (MBs) is activated by target DNA in the presence of exonuclease-III (Exo-III), achieving the concept of exonuclease-assisted cascaded recycling amplification (Exo-CRA) for DNA detection with a wide dynamic range of 8 orders of magnitude.     

An electrochemical microRNA biosensor based on protein p19 combining an acridone derivate as indicator and DNA concatamers for signal amplification

The new acridone derivative 5, 7-dinitro-2-sulfo-acridone (DSA) with excellent electrochemical activity was synthesized and reported for the first time in this paper. Then an electrochemical biosensor was fabricated for the signal amplified detection of microRNA (miRNA) via applying home-made DSA as signal unit. The p19 protein-functionalized magnetic beads (PFMBs) for specific recognition and enrichment of miRNA. Then DSA is combined with the long DNA concatamers, which functions as a signal enhancement platform to facilitate the high selectivity and sensitivity determination of miRNA. The usage of this novel electrochemical activity made a contribution to the performance of the approach, such as achieving a detection limit of 6 aM. To the best of our knowledge, this is the first attempt to apply DSA, PFMBs and long DNA concatamers for the fabrication of the electrochemical biosensors, which may represent a promising path toward early diagnosis of cancer at the point of care.     

An electrochemical biosensor for direct detection of DNA using polystyrene-g-soya oil-g-imidazole graft copolymer

A label-free electrochemical DNA biosensor was developed through the attachment of polystyrene-g-soya oil-g-imidazole graft copolymer (PS-PSyIm) onto modified graphene oxide (GO) electrodeposited on glassy carbon electrode (GC). GC/GO electrode was initially functionalised via electrochemical reduction of 4-nitrobenzene diazonium salt, followed by the electrochemical reduction of NO₂ to NH₂. Subsequent to the electrochemical deposition of gold nanoparticles on modified surface, the attachment of the PS-PSyIm graft copolymer on the resulting electrode was achieved. The interaction of PS-PSyIm with DNA at the bare glassy carbon electrode was studied by cyclic voltammetry technique, and it was found that interaction predominantly takes place through intercalation mode. The selectivity of developed DNA biosensor was also explored by DPV on the basis of considering hybridisation event with non-complementary, one-base mismatched DNA and complementary target DNA sequence. Large decrease in the peak current was found upon the addition of complementary target DNA. The sensitivity of the developed DNA biosensor was also investigated, and detection limit was found to be 1.20 nmol L^?1.